INFO 2025-06-26 15:32:01,222 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 15:32:01,222 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Autonomy mission - ctdToUse = ctd1 INFO 2025-06-26 15:32:01,222 process.py process_mission():449 [1] Processing AUVCTD mission 2010.082.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 15:32:01,223 process.py download_process():165 [1] Download and processing steps for 2010.082.02 INFO 2025-06-26 15:32:01,223 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2010/2010082/2010.082.02 INFO 2025-06-26 15:32:01,223 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2010/2010082/2010.082.02 to /data/auv_data/dorado/missionlogs/2010.082.02 INFO 2025-06-26 15:32:06,763 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2010.082.02 INFO 2025-06-26 15:32:06,763 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.082.02/ctdDriver.log (9301254 bytes) INFO 2025-06-26 15:32:07,445 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.082.02/ctdDriver.log: [ 439 679 722 1034 1336 1722 2641 3248 3304 3492 4633 7816 8050 9249 10078 10590 10741 15977 16910 18257 18541 24657 26160 26595 27847 28926 34582 36436 39892 52678 54279 58015 64332 68715 71423 72978 74001 85610 95984] INFO 2025-06-26 15:32:07,474 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.082.02/ctdDriver2.log (9300671 bytes) INFO 2025-06-26 15:32:08,154 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.082.02/ctdDriver2.log: [ 5 438 530 910 1335 1721 2359 2641 3036 3247 3303 3491 4632 7812 8046 10073 10735 15270 15971 17788 18252 18536 21412 26593 28923 34580 37795 45304 54274 58010 61989 68708 83917 92556 95978 96525] INFO 2025-06-26 15:32:08,183 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.082.02/gps.log (125780 bytes) INFO 2025-06-26 15:32:08,205 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.082.02/hydroscatlog.log (8143234 bytes) INFO 2025-06-26 15:32:09,019 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.082.02/hydroscatlog.log: [ 1 76 80 158 160 302 380 668 764 800 943 1514 1516 1670 1671 1804 2051 2132 2223 3610 3756 3758 4802 4985 5268 5269 5270 5622 7810 7901 8137 8770 9533 10160 10163 11851 12046 13982 14270 15100 16991 17843 19370 24130 24736 25507 25680 25831 26674 29948 31153 32983 34818 39966 40311 40316 42426 43377 43938 44414 44558 45380 45406 51137 52550 52746 55023 55523 58035 59820 60974 62060 65237 73793 79938 81275 84945 87837 88196 88654 89075 89077 94084] INFO 2025-06-26 15:32:09,039 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.082.02/navigation.log (28487686 bytes) INFO 2025-06-26 15:32:11,029 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.082.02/isuslog.log (341 bytes) INFO 2025-06-26 15:32:11,034 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.082.02/isuslog.log: [1] INFO 2025-06-26 15:32:11,034 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.082.02/parosci.log (9467750 bytes) INFO 2025-06-26 15:32:11,831 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.082.02/tailCone.log (5794987 bytes) INFO 2025-06-26 15:32:12,538 logs2netcdfs.py download_process_logs():807 [1] Time to process: 5.77 seconds INFO 2025-06-26 15:32:12,538 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2010.082.02/lopc.bin (16608532 bytes) INFO 2025-06-26 15:32:12,538 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 15:32:12 2025 INFO 2025-06-26 15:32:12,538 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2010.082.02/parosci.nc INFO 2025-06-26 15:32:12,538 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 15:32:12,538 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2010.082.02/parosci.nc INFO 2025-06-26 15:32:12,542 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1269357074.9, sensor_off_time = 1269381325.2 INFO 2025-06-26 15:32:12,542 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 24250 seconds. Expecting to read 48500 L frames from the lopc.bin file. INFO 2025-06-26 15:32:12,542 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 48500 records from the lopc.bin file. INFO 2025-06-26 15:32:12,826 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2010-03-23 15:11:14 Z and endTime = 2010-03-23 21:55:25 Z with 48500 records expected to be read from lopc.bin INFO 2025-06-26 15:32:12,827 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2010.082.02/lopc.bin INFO 2025-06-26 15:32:12,827 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2010.082.02/lopc.nc INFO 2025-06-26 15:32:12,827 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2010.082.02/lopc.nc INFO 2025-06-26 15:32:12,827 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2010.082.02 INFO 2025-06-26 15:32:12,828 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 15:32:12,831 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A075301 WARNING 2025-06-26 15:32:12,831 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 15:32:12,877 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 15:32:12,877 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 15:32:12,877 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 15:32:16,560 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 13337 7867 1 0 0 0 86 3.7 seconds, last L Frame: 48500 INFO 2025-06-26 15:32:20,340 lopcToNetCDF.py unpackLOPCbin():1013 [1] 20000 23415 16470 1 0 0 0 164 3.8 seconds, last L Frame: 48500 INFO 2025-06-26 15:32:24,274 lopcToNetCDF.py unpackLOPCbin():1013 [1] 30000 33519 25464 1 0 0 0 268 3.9 seconds, last L Frame: 48500 INFO 2025-06-26 15:32:28,402 lopcToNetCDF.py unpackLOPCbin():1013 [1] 40000 43615 34837 1 0 0 0 364 4.1 seconds, last L Frame: 48500 ERROR 2025-06-26 15:32:29,856 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 15:32:29,858 process.py calibrate():227 [1] Calibration steps for 2010.082.02 INFO 2025-06-26 15:32:30,134 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 15:32:30,136 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 15:32:30,808 calibrate.py _nudge_pos():1806 [1] 110: 0.010 0.0037358 -0.0021720 9648 32.43 17.099 -12.411 2010-03-23T15:45:24.050447616 INFO 2025-06-26 15:32:30,847 calibrate.py _nudge_pos():1806 [1] 114: 0.020 0.0000794 0.0000319 95 0.31 37.593 18.882 2010-03-23T15:45:46.048940544 INFO 2025-06-26 15:32:32,321 calibrate.py _nudge_pos():1806 [1] 269: 0.020 -0.0011192 0.0019507 10431 34.85 -4.766 10.373 2010-03-23T16:23:11.055147264 INFO 2025-06-26 15:32:32,341 calibrate.py _nudge_pos():1806 [1] 271: 0.020 0.0000139 -0.0000300 105 0.35 5.938 -16.051 2010-03-23T16:23:33.053640448 INFO 2025-06-26 15:32:33,048 calibrate.py _nudge_pos():1806 [1] 346: 0.030 -0.0000031 0.0000082 55 0.18 -2.536 8.403 2010-03-23T16:24:58.047817728 INFO 2025-06-26 15:32:33,801 calibrate.py _nudge_pos():1806 [1] 423: 0.020 0.0029582 -0.0035231 9649 32.25 13.617 -20.245 2010-03-23T16:58:29.050054656 INFO 2025-06-26 15:32:35,329 calibrate.py _nudge_pos():1806 [1] 580: 0.030 0.0004663 0.0043647 10446 34.86 1.985 23.199 2010-03-23T17:35:59.055918592 INFO 2025-06-26 15:32:36,791 calibrate.py _nudge_pos():1806 [1] 730: 0.020 0.0033735 -0.0031788 10129 33.81 14.808 -17.420 2010-03-23T18:12:17.056715520 INFO 2025-06-26 15:32:38,347 calibrate.py _nudge_pos():1806 [1] 891: 0.030 0.0002504 0.0002862 10194 34.03 1.092 1.558 2010-03-23T18:48:59.055868160 INFO 2025-06-26 15:32:39,924 calibrate.py _nudge_pos():1806 [1] 1051: 0.040 0.0044017 -0.0023840 10232 34.18 19.116 -12.925 2010-03-23T19:25:49.054472960 INFO 2025-06-26 15:32:41,613 calibrate.py _nudge_pos():1806 [1] 1220: 0.050 -0.0002413 0.0003954 10441 34.86 -1.027 2.102 2010-03-23T20:03:29.049652480 INFO 2025-06-26 15:32:41,674 calibrate.py _nudge_pos():1806 [1] 1226: 0.050 0.0000091 -0.0000021 75 0.25 5.489 -1.595 2010-03-23T20:03:49.048282624 INFO 2025-06-26 15:32:42,069 calibrate.py _nudge_pos():1806 [1] 1266: 0.040 -0.0000189 0.0000454 15 0.05 -60.113 180.218 2010-03-23T20:04:33.055267840 INFO 2025-06-26 15:32:43,144 calibrate.py _nudge_pos():1806 [1] 1374: 0.050 0.0029379 -0.0020131 10706 35.75 12.199 -10.435 2010-03-23T20:42:05.050995712 INFO 2025-06-26 15:32:44,829 calibrate.py _nudge_pos():1806 [1] 1542: 0.060 -0.0002168 -0.0001939 10041 33.51 -0.960 -1.072 2010-03-23T21:18:23.051792384 INFO 2025-06-26 15:32:46,565 calibrate.py _nudge_pos():1806 [1] 1714: 0.060 0.0039021 -0.0017178 10136 33.85 17.112 -9.404 2010-03-23T21:55:05.050945024 INFO 2025-06-26 15:32:46,771 calibrate.py _nudge_pos():1862 [1] 1684: - - - 0 0.00 - - INFO 2025-06-26 15:32:46,771 calibrate.py _nudge_pos():1868 [1] Points in final series = 120701 WARNING 2025-06-26 15:32:46,942 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 15:32:59,794 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:33:06,641 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:33:07,377 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:33:07,380 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2010.082.02/ctd1.nc INFO 2025-06-26 15:33:07,381 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 15:33:07,381 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 15:33:07,381 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 15:33:12,683 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:33:13,405 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:33:13,407 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2010.082.02/ctd2.nc INFO 2025-06-26 15:33:13,408 calibrate.py _range_qc_combined_nc():898 [1] Setting 169 ctd2_salinity values to NaN INFO 2025-06-26 15:33:13,409 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 15:33:13,409 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 15:33:13,415 calibrate.py process_logs():3542 [1] Error processing biolume: biolume has no orig_data - likely a missing or zero-sized .log file in missionlogs/2010.082.02 ERROR 2025-06-26 15:33:13,415 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2010.082.02 ERROR 2025-06-26 15:33:13,415 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2010.082.02 INFO 2025-06-26 15:33:13,509 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2010.082.02/dorado_2010.082.02_cal.nc INFO 2025-06-26 15:33:24,052 calibrate.py write_netcdf():3512 [1] Data variables written: ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 15:33:24,059 process.py align():251 [1] Alignment steps for 2010.082.02 INFO 2025-06-26 15:33:24,088 align.py process_cal():139 [1] Processing dorado_2010.082.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2010.082.02 INFO 2025-06-26 15:33:24,122 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:33:24,126 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 15:33:24,207 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:33:24,212 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 15:33:24,292 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:33:24,297 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 15:33:24,345 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 15:33:24,345 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 15:33:24,375 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:33:24,380 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 15:33:24,462 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:24,467 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 15:33:24,536 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:24,541 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 15:33:24,611 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:24,616 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 15:33:24,684 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:24,689 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:24,758 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:24,763 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:24,832 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:24,837 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:24,908 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:24,913 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:24,981 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:24,986 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:25,059 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:25,064 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:25,132 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:25,137 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:25,207 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:25,212 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:25,280 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:25,286 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:25,355 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:25,360 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:25,428 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:25,433 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:25,505 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:25,510 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:25,580 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:25,585 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:25,657 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:25,662 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:25,731 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:25,736 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:25,807 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:25,812 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:25,881 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:25,886 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:25,957 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:25,962 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:26,034 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.082.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:33:26,039 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:33:26,122 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.13 INFO 2025-06-26 15:33:26,168 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.13 INFO 2025-06-26 15:33:26,215 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.13 INFO 2025-06-26 15:33:26,264 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 15:33:26,321 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2010.082.02/dorado_2010.082.02_align.nc INFO 2025-06-26 15:33:26,404 align.py write_netcdf():342 [1] Data variables written: ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 15:33:26,406 process.py resample():273 [1] Resampling steps for 2010.082.02 INFO 2025-06-26 15:33:26,407 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 15:33:26,431 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.082.02/dorado_2010.082.02_align.nc mission netCDF file INFO 2025-06-26 15:33:26,437 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.082.02/dorado_2010.082.02_align.nc mission netCDF file INFO 2025-06-26 15:33:26,438 resample.py get_mission_start_end():1145 [1] navigation: 2010-03-23T15:12:00.897673216 to 2010-03-23T21:55:25.049575168 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 15:33:26,440 resample.py get_mission_start_end():1145 [1] hs2 : 2010-03-23T15:11:21.780352768 to 2010-03-23T21:55:25.139568896 (0 days 00:00:00 before mission_end) INFO 2025-06-26 15:33:26,442 resample.py get_mission_start_end():1145 [1] ctd1 : 2010-03-23T15:11:39.849114880 to 2010-03-23T21:55:25.079572992 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 15:33:26,443 resample.py get_mission_start_end():1145 [1] ctd2 : 2010-03-23T15:11:40.469072640 to 2010-03-23T21:55:24.989579264 (0 days 00:00:00.149989632 before mission_end) INFO 2025-06-26 15:33:26,445 resample.py get_mission_start_end():1145 [1] isus : 2010-03-23T15:12:17.296549632 to 2010-03-23T15:12:24.846032384 (0 days 06:43:00.293536512 before mission_end) WARNING 2025-06-26 15:33:26,446 resample.py get_mission_start_end():1156 [1] Instrument isus has a gap > 5 minutes at the end of the mission: 0 days 06:43:00.293536512 INFO 2025-06-26 15:33:26,447 resample.py get_mission_start_end():1145 [1] tailcone : 2010-03-23T15:11:12.181010432 to 2010-03-23T21:55:25.019577088 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 15:33:26,448 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.082.02/dorado_2010.082.02_align.nc mission netCDF file INFO 2025-06-26 15:33:26,448 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:26,715 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:26,760 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:26,804 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:26,847 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:26,885 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:26,923 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:26,960 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:26,996 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,032 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,067 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,101 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,136 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,171 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,206 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,241 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,275 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,309 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,347 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,383 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,422 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,458 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,495 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,531 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,568 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,580 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,581 resample.py resample_variable():1038 [1] Padding isus_nitrate with 0 days 06:43:00.293536512 of NaNs to the end of mission INFO 2025-06-26 15:33:27,592 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,592 resample.py resample_variable():1038 [1] Padding isus_temp with 0 days 06:43:00.293536512 of NaNs to the end of mission INFO 2025-06-26 15:33:27,602 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,602 resample.py resample_variable():1038 [1] Padding isus_quality with 0 days 06:43:00.293536512 of NaNs to the end of mission INFO 2025-06-26 15:33:27,645 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 15:33:27,888 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2010.082.02/dorado_2010.082.02_1S.nc INFO 2025-06-26 15:33:30,015 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 15:33:34,461 create_products.py gulper_odv():522 [1] Wrote 4 Gulper data lines to /data/auv_data/dorado/missionodvs/2010.082.02/dorado_2010.082.02_1S_Gulper.txt INFO 2025-06-26 15:33:34,461 process.py archive():337 [1] Archiving steps for 2010.082.02 INFO 2025-06-26 15:33:34,462 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2010.082.02/dorado_2010.082.02, BASE_PATH = /data/auv_data INFO 2025-06-26 15:33:34,463 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2010.082.02/dorado_2010.082.02 files to /Volumes/AUVCTD/surveys/2010/netcdf INFO 2025-06-26 15:33:34,464 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.082.02_1S.nc INFO 2025-06-26 15:33:34,483 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.082.02/dorado_2010.082.02_1S.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 15:33:34,484 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.082.02_cal.nc INFO 2025-06-26 15:33:34,586 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.082.02/dorado_2010.082.02_cal.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 15:33:34,587 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.082.02_align.nc INFO 2025-06-26 15:33:34,673 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.082.02/dorado_2010.082.02_align.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 15:33:34,703 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.082.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010082/2010.082.02 done. INFO 2025-06-26 15:33:34,729 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.082.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010082/2010.082.02 done. INFO 2025-06-26 15:33:34,734 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.082.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010082/2010.082.02 done. INFO 2025-06-26 15:33:34,759 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.082.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010082/2010.082.02 done. INFO 2025-06-26 15:33:34,836 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.082.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010082/2010.082.02 done. INFO 2025-06-26 15:33:34,840 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.082.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010082/2010.082.02 done. INFO 2025-06-26 15:33:34,866 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.082.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010082/2010.082.02 done. INFO 2025-06-26 15:33:34,888 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.082.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010082/2010.082.02 done. INFO 2025-06-26 15:33:34,954 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.082.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010082/2010.082.02 done. INFO 2025-06-26 15:33:34,954 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 15:33:34,956 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2010/odv/dorado_2010.082.02_1S_Gulper.txt INFO 2025-06-26 15:33:34,961 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2010.082.02/dorado_2010.082.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2010/odv done. INFO 2025-06-26 15:33:34,961 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.082.02/dorado_2010.082.02_processing.log /Volumes/AUVCTD/surveys/2010/netcdf